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Abstract: Nutrient loss from purple soils has been reported to increase pollution of the Yangtze River. However, few studies have addressed the variations of nutrient concentration in runoff during natural rainstorms in the regions. Nitrogen and phosphorus concentrations in runoff waters from a small agricultural watershed, in the purple soil region of southwest China, were investigated for four natural rainstorms occurred in a conventional double cropping system (wheat–corn) and another six rainstorms in a new triple cropping system (wheat–corn–sweet potato). The NO3 − concentrations in runoff for the observed rainstorms generally varied from 1.0 to 3.5gm−3, which were noticeably affected by flow rates. A significant logarithmic correlation between NO3 − concentrations and flow rates for each rainstorm was identified. In contrast, the concentrations of NH4 + and dissolved reactive phosphorus (DRP) in runoff fluctuated substantially without a noticeable trend for each rainstorm. Positive linear correlation between the concentrations of DRP and sediment for each rainstorm tested was found under the circumstances of double cropping system. In addition, the ratios of NO3 − to NH4 + for the loss amount in 10 rainstorms varied from 1 to 7 for the triple cropping system and 16–29 for the double cropping system. Furthermore, the ratios of the sum of NO3 − and NH4 + to DRP for the loss amount in 10 rainstorms ranged from 12 to 79 depending on the cropping systems. Nitrate nitrogen was proved to be the main form of inorganic nitrogen loss in runoff water in the purple soil region. Compared with the conventional double cropping system, the new triple cropping system tends to cause more NH4 + loss. These findings would help develop the effective erosion control strategies and select a suitable cropping system to reduce potential pollution hazards. [Copyright &y& Elsevier]